Merge Samtools and Freebayes vcf files

Question

[kspata]

Hi,

I am analyzing presence of variants in exonic regions of 10 genes. I have sequencing data for samples obtained from different individuals. I aligned the NextSeq PE 150 sequencing data to hg38 human genome assembly using bowtie2 and called variants using samtools and freebayes and filtered variants for exonic regions using bedtools intersect.

I observed some common variants between samtools and freebayes vcf and unique variants in both files. I visualized these variants from both files using IGV which confirms their presence.

Can I merge these two variant files obtained from different tools? If so how can I merge the vcf file?

Answer 1

[Pierre Lindenbaum]

gatk CombineVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php with the option genotypemergeoption

UNIQUIFY
    Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
PRIORITIZE
    Take genotypes in priority order (see the priority argument).
UNSORTED
    Take the genotypes in any order.
REQUIRE_UNIQUE
    Require that all samples/genotypes be unique between all inputs.